Changeset 7047


Ignore:
Timestamp:
10/07/10 22:48:36 (9 years ago)
Author:
curtis
Message:

Backport latest loci-plugins trunk to Maven branch.

Location:
branches/maven/projects/loci-plugins/src/main
Files:
73 edited

Legend:

Unmodified
Added
Removed
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins

  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/About.java

    r6588 r7047  
    3737 * 
    3838 * <dl><dt><b>Source code:</b></dt> 
    39  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/About.java">Trac</a>, 
    40  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/About.java">SVN</a></dd></dl> 
     39 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/About.java">Trac</a>, 
     40 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/About.java">SVN</a></dd></dl> 
    4141 */ 
    4242public final class About implements PlugIn { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/BF.java

    r6588 r7047  
    4141 * 
    4242 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/BF.java">Trac</a>, 
    44  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/BF.java">SVN</a></dd></dl> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/BF.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/BF.java">SVN</a></dd></dl> 
    4545 */ 
    4646public final class BF { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/LociExporter.java

    r6588 r7047  
    4141 * 
    4242 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/LociExporter.java">Trac</a>, 
    44  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/LociExporter.java">SVN</a></dd></dl> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/LociExporter.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/LociExporter.java">SVN</a></dd></dl> 
    4545 * 
    4646 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/LociImporter.java

    r6588 r7047  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/LociImporter.java">Trac</a>, 
    42  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/LociImporter.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/LociImporter.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/LociImporter.java">SVN</a></dd></dl> 
    4343 * 
    4444 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/Slicer.java

    r6654 r7047  
    4545 * 
    4646 * <dl><dt><b>Source code:</b></dt> 
    47  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">Trac</a>, 
    48  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">SVN</a></dd></dl> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/Slicer.java">SVN</a></dd></dl> 
    4949 * 
    5050 * @author Melissa Linkert melissa at glencoesoftware.com 
     
    110110 
    111111      if (imp.isComposite()) { 
    112         LUT lut = ((CompositeImage) imp).getChannelLut(zct[1] + 1); 
    113         newStacks[i].setColorModel(lut); 
     112        CompositeImage composite = (CompositeImage) imp; 
     113        if (composite.getMode() == CompositeImage.COLOR) { 
     114          LUT lut = composite.getChannelLut(zct[1] + 1); 
     115          newStacks[i].setColorModel(lut); 
     116        } 
    114117      } 
    115118 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/Updater.java

    r6588 r7047  
    4848 * 
    4949 * <dl><dt><b>Source code:</b></dt> 
    50  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/Updater.java">Trac</a>, 
    51  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/Updater.java">SVN</a></dd></dl> 
     50 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/Updater.java">Trac</a>, 
     51 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/Updater.java">SVN</a></dd></dl> 
    5252 * 
    5353 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/ConfigWindow.java

    r6654 r7047  
    4040import java.util.Date; 
    4141import java.util.HashMap; 
     42import java.util.Properties; 
    4243 
    4344import javax.imageio.spi.IIORegistry; 
     
    7071 * 
    7172 * <dl><dt><b>Source code:</b></dt> 
    72  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java">Trac</a>, 
    73  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java">SVN</a></dd></dl> 
     73 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java">Trac</a>, 
     74 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/ConfigWindow.java">SVN</a></dd></dl> 
    7475 * 
    7576 * @author Curtis Rueden ctrueden at wisc.edu 
     
    294295    log.println("LOCI Plugins configuration - " + new Date()); 
    295296 
     297    // list system properties 
     298    log.println(); 
     299    log.println("-- System properties --"); 
     300    Properties sysProps = System.getProperties(); 
     301    for (Object name : sysProps.keySet()) { 
     302      log.println(name + " = " + sysProps.getProperty(name.toString())); 
     303    } 
     304 
    296305    // generate list of formats 
    297306    log.println(); 
     
    326335    String qtVersion = null; 
    327336    try { 
    328       Class<?> qtToolsClass = Class.forName("loci.formats.LegacyQTTools"); 
     337      Class<?> qtToolsClass = Class.forName("loci.formats.gui.LegacyQTTools"); 
    329338      Object qtTools = qtToolsClass.newInstance(); 
    330339      Method getQTVersion = qtToolsClass.getMethod("getQTVersion"); 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/FlexWidgets.java

    r6654 r7047  
    4343 * 
    4444 * <dl><dt><b>Source code:</b></dt> 
    45  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/FlexWidgets.java">Trac</a>, 
    46  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/FlexWidgets.java">SVN</a></dd></dl> 
     45 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/FlexWidgets.java">Trac</a>, 
     46 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/FlexWidgets.java">SVN</a></dd></dl> 
    4747 * 
    4848 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/FormatEntry.java

    r6654 r7047  
    3434 * 
    3535 * <dl><dt><b>Source code:</b></dt> 
    36  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/FormatEntry.java">Trac</a>, 
    37  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/FormatEntry.java">SVN</a></dd></dl> 
     36 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/FormatEntry.java">Trac</a>, 
     37 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/FormatEntry.java">SVN</a></dd></dl> 
    3838 * 
    3939 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/IFormatWidgets.java

    r6588 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/IFormatWidgets.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/IFormatWidgets.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/IFormatWidgets.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/IFormatWidgets.java">SVN</a></dd></dl> 
    3636 * 
    3737 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/InstallWizard.java

    r6773 r7047  
    4242 * 
    4343 * <dl><dt><b>Source code:</b></dt> 
    44  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/InstallWizard.java">Trac</a>, 
    45  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/InstallWizard.java">SVN</a></dd></dl> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/InstallWizard.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/InstallWizard.java">SVN</a></dd></dl> 
    4646 * 
    4747 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/LibraryEntry.java

    r6654 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LibraryEntry.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LibraryEntry.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LibraryEntry.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LibraryEntry.java">SVN</a></dd></dl> 
    3939 * 
    4040 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/LociConfig.java

    r6588 r7047  
    3333 * 
    3434 * <dl><dt><b>Source code:</b></dt> 
    35  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LociConfig.java">Trac</a>, 
    36  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LociConfig.java">SVN</a></dd></dl> 
     35 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LociConfig.java">Trac</a>, 
     36 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LociConfig.java">SVN</a></dd></dl> 
    3737 * 
    3838 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/LociInstaller.java

    r6588 r7047  
    3434 * 
    3535 * <dl><dt><b>Source code:</b></dt> 
    36  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LociInstaller.java">Trac</a>, 
    37  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LociInstaller.java">SVN</a></dd></dl> 
     36 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/LociInstaller.java">Trac</a>, 
     37 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/LociInstaller.java">SVN</a></dd></dl> 
    3838 * 
    3939 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/ND2Widgets.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/ND2Widgets.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/ND2Widgets.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/ND2Widgets.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/ND2Widgets.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/PictWidgets.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/PictWidgets.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/PictWidgets.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/PictWidgets.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/PictWidgets.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/QTWidgets.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/QTWidgets.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/QTWidgets.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/QTWidgets.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/QTWidgets.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/SDTWidgets.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/SDTWidgets.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/SDTWidgets.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/SDTWidgets.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/SDTWidgets.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/SpringUtilities.java

    r6588 r7047  
    7070 * 
    7171 * <dl><dt><b>Source code:</b></dt> 
    72  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/SpringUtilities.java">Trac</a>, 
    73  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/SpringUtilities.java">SVN</a></dd></dl> 
     72 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/SpringUtilities.java">Trac</a>, 
     73 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/SpringUtilities.java">SVN</a></dd></dl> 
    7474 */ 
    7575public class SpringUtilities { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/TextAreaWriter.java

    r6588 r7047  
    3434 * 
    3535 * <dl><dt><b>Source code:</b></dt> 
    36  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/TextAreaWriter.java">Trac</a>, 
    37  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/TextAreaWriter.java">SVN</a></dd></dl> 
     36 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/TextAreaWriter.java">Trac</a>, 
     37 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/TextAreaWriter.java">SVN</a></dd></dl> 
    3838 * 
    3939 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/config/TiffDelegateWidgets.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/TiffDelegateWidgets.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/TiffDelegateWidgets.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/config/TiffDelegateWidgets.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/config/TiffDelegateWidgets.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/Calibrator.java

    r6656 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Calibrator.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Calibrator.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Calibrator.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Calibrator.java">SVN</a></dd></dl> 
    4444 */ 
    4545public class Calibrator { 
     
    7474    if (td != null) tcal = td.floatValue(); 
    7575 
     76    double xPosition = Double.NaN; 
     77    double yPosition = Double.NaN; 
     78    double zPosition = Double.NaN; 
     79    if (meta.getPlaneCount(series) > 0) { 
     80      Double posX = meta.getPlanePositionX(series, 0); 
     81      Double posY = meta.getPlanePositionY(series, 0); 
     82      Double posZ = meta.getPlanePositionZ(series, 0); 
     83      if (posX != null) xPosition = posX.doubleValue(); 
     84      if (posY != null) yPosition = posY.doubleValue(); 
     85      if (posZ != null) zPosition = posZ.doubleValue(); 
     86    } 
     87 
    7688    boolean xcalPresent = !Double.isNaN(xcal); 
    7789    boolean ycalPresent = !Double.isNaN(ycal); 
     
    93105    tcalPresent = !Double.isNaN(tcal); 
    94106    final boolean hasSpatial = xcalPresent || ycalPresent || zcalPresent; 
    95     final boolean hasCalibration = hasSpatial || ycalPresent; 
     107    final boolean hasStageData = 
     108      !Double.isNaN(xPosition) || !Double.isNaN(yPosition); 
     109    final boolean hasCalibration = hasSpatial || ycalPresent || hasStageData; 
    96110 
    97111    if (hasCalibration) { 
     
    103117      if (zcalPresent) cal.pixelDepth = zcal; 
    104118      if (tcalPresent) cal.frameInterval = tcal; 
     119      if (!Double.isNaN(xPosition) && xcalPresent) { 
     120        cal.xOrigin = xPosition * (1 / xcal); 
     121      } 
     122      if (!Double.isNaN(yPosition) && ycalPresent) { 
     123        cal.yOrigin = yPosition * (1 / ycal); 
     124      } 
     125      if (!Double.isNaN(zPosition) && zcalPresent) { 
     126        cal.zOrigin = zPosition * (1 / zcal); 
     127      } 
    105128      imp.setCalibration(cal); 
    106129    } 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ColorDialog.java

    r6588 r7047  
    5151 * 
    5252 * <dl><dt><b>Source code:</b></dt> 
    53  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">Trac</a>, 
    54  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">SVN</a></dd></dl> 
     53 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">Trac</a>, 
     54 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">SVN</a></dd></dl> 
    5555 * 
    5656 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/Colorizer.java

    r6668 r7047  
    5454 * 
    5555 * <dl><dt><b>Source code:</b></dt> 
    56  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Colorizer.java">Trac</a>, 
    57  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Colorizer.java">SVN</a></dd></dl> 
     56 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Colorizer.java">Trac</a>, 
     57 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Colorizer.java">SVN</a></dd></dl> 
    5858 * 
    5959 * @author Melissa Linkert melissa at glencoesoftware.com 
     
    161161        // NB: Cannot use CompositeImage for some reason. 
    162162        if (luts != null && luts.length > 0 && luts[0] != null) { 
    163           imp.getProcessor().setColorModel(luts[0]); 
     163          if (imp instanceof VirtualImagePlus) { 
     164            ((VirtualImagePlus) imp).setLUTs(luts); 
     165          } 
     166          else if (cSize == 1) imp.getProcessor().setColorModel(luts[0]); 
    164167        } 
    165168        if (mode != -1 && cSize > 7) { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/Concatenator.java

    r6654 r7047  
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">SVN</a></dd></dl> 
     38 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">Trac</a>, 
     39 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Concatenator.java">SVN</a></dd></dl> 
    4040 * 
    4141 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/CropDialog.java

    r6654 r7047  
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">SVN</a></dd></dl> 
     38 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">Trac</a>, 
     39 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/CropDialog.java">SVN</a></dd></dl> 
    4040 */ 
    4141public class CropDialog extends ImporterDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/DisplayHandler.java

    r6704 r7047  
    5858 * 
    5959 * <dl><dt><b>Source code:</b></dt> 
    60  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">Trac</a>, 
    61  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">SVN</a></dd></dl> 
     60 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">Trac</a>, 
     61 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/DisplayHandler.java">SVN</a></dd></dl> 
    6262 * 
    6363 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/FilePatternDialog.java

    r6654 r7047  
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">SVN</a></dd></dl> 
     38 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">Trac</a>, 
     39 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">SVN</a></dd></dl> 
    4040 */ 
    4141public class FilePatternDialog extends ImporterDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/IdDialog.java

    r6654 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/IdDialog.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class IdDialog extends ImporterDialog { 
     
    5555  @Override 
    5656  protected boolean needPrompt() { 
    57     return !process.isWindowless() && options.getId() == null; 
     57    return options.getId() == null; 
    5858  } 
    5959 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImagePlusReader.java

    r6716 r7047  
    6363 * 
    6464 * <dl><dt><b>Source code:</b></dt> 
    65  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">Trac</a>, 
    66  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">SVN</a></dd></dl> 
     65 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">Trac</a>, 
     66 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java">SVN</a></dd></dl> 
    6767 */ 
    6868public class ImagePlusReader implements StatusReporter { 
     
    155155    final ImagePlus imp = new ImagePlus(title, stack); 
    156156 
    157     // NB: Save individual planar LUTs as properties, for later access. 
    158     // This step is necessary because ImageStack.addSlice only extracts the 
    159     // pixels from the ImageProcessor, and does not preserve the ColorModel. 
    160     // Later, Colorizer can use the LUTs when wrapping into a CompositeImage. 
    161     for (int i=0; i<luts.size(); i++) { 
    162       final LUT lut = luts.get(i); 
    163       if (lut != null) imp.setProperty(PROP_LUT + i, lut); 
    164     } 
    165  
     157    saveLUTs(imp, luts); 
    166158    return imp; 
    167159  } 
     
    255247    // create image stack 
    256248    final ImageStack stack; 
    257     if (options.isVirtual()) stack = createVirtualStack(process, s); 
     249    if (options.isVirtual()) stack = createVirtualStack(process, s, luts); 
    258250    else stack = readPlanes(process, s, luts); 
    259251 
     
    273265      vip.setReader(reader); 
    274266      imp = vip; 
     267      saveLUTs(imp, luts); 
    275268    } 
    276269    else imp = createImage(title, stack, luts); 
     
    296289  } 
    297290 
    298   private ImageStack createVirtualStack(ImportProcess process, int s) 
    299     throws FormatException, IOException 
     291  private ImageStack createVirtualStack(ImportProcess process, int s, 
     292    List<LUT> luts) throws FormatException, IOException 
    300293  { 
    301294    final ImporterOptions options = process.getOptions(); 
     
    316309      virtualStack.addSlice(label); 
    317310    } 
     311 
     312    if (luts != null) { 
     313      for (int c=0; c<cCount; c++) { 
     314        int index = reader.getIndex(0, c, 0); 
     315        ImageProcessor ip = reader.openProcessors(index)[0]; 
     316        final ColorModel cm = ip.getColorModel(); 
     317        final LUT lut = cm instanceof LUT ? (LUT) cm : null; 
     318        luts.add(lut); 
     319      } 
     320    } 
     321 
    318322    return virtualStack; 
    319323  } 
     
    591595  } 
    592596 
     597  private static void saveLUTs(ImagePlus imp, List<LUT> luts) { 
     598    // NB: Save individual planar LUTs as properties, for later access. 
     599    // This step is necessary because ImageStack.addSlice only extracts the 
     600    // pixels from the ImageProcessor, and does not preserve the ColorModel. 
     601    // Later, Colorizer can use the LUTs when wrapping into a CompositeImage. 
     602    for (int i=0; i<luts.size(); i++) { 
     603      final LUT lut = luts.get(i); 
     604      if (lut != null) { 
     605        imp.setProperty(PROP_LUT + i, lut); 
     606      } 
     607    } 
     608  } 
     609 
    593610} 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImportProcess.java

    r6716 r7047  
    2929import java.util.ArrayList; 
    3030import java.util.List; 
     31import java.util.StringTokenizer; 
    3132 
    3233import loci.common.Location; 
     
    7172 * 
    7273 * <dl><dt><b>Source code:</b></dt> 
    73  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java">Trac</a>, 
    74  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java">SVN</a></dd></dl> 
     74 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java">Trac</a>, 
     75 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java">SVN</a></dd></dl> 
    7576 */ 
    7677public class ImportProcess implements StatusReporter { 
     
    180181    if (options.isWindowless()) return true; // globally windowless 
    181182    return baseReader != null && LociPrefs.isWindowless(baseReader); 
     183  } 
     184 
     185  public void setSeriesList(String seriesList) { 
     186    final int seriesCount = getSeriesCount(); 
     187    options.clearSeries(); 
     188 
     189    // remove illegal characters 
     190    seriesList = seriesList.replaceAll("[^\\d,\\-]", ""); 
     191 
     192    // parse series list 
     193    StringTokenizer st = new StringTokenizer(seriesList, ","); 
     194    while (st.hasMoreTokens()) { 
     195      final String token = st.nextToken(); 
     196      int dash = token.indexOf("-"); 
     197      if (dash < 0) { 
     198        // single number 
     199        try { 
     200          final int s = Integer.parseInt(token) - 1; 
     201          options.setSeriesOn(s, true); 
     202        } 
     203        catch (NumberFormatException exc) { 
     204          // skip invalid series number 
     205        } 
     206      } 
     207      else { 
     208        // numerical range 
     209        final String firstString = token.substring(0, dash); 
     210        final String lastString = token.substring(dash + 1); 
     211        try { 
     212          final int first = Integer.parseInt(firstString) - 1; 
     213          final int last = Integer.parseInt(lastString) - 1; 
     214          for (int s = first; s <= last; s++) { 
     215            if (s >= seriesCount) break; // skip out of bounds series 
     216            options.setSeriesOn(s, true); 
     217          } 
     218        } 
     219        catch (NumberFormatException exc) { 
     220          // skip invalid numerical range 
     221        } 
     222      } 
     223    } 
    182224  } 
    183225 
     
    443485      // overwrite base filename with file pattern 
    444486      String id = options.getId(); 
    445       if (id == null) id = getCurrentFile(); 
    446       FilePattern fp = fileStitcher.findPattern(id); 
    447       if (fp.isValid()) id = fp.getPattern(); 
    448       else id = getCurrentFile(); 
    449487      options.setId(id); 
    450488      fileStitcher.setUsingPatternIds(true); 
    451489    } 
    452490    r.setId(options.getId()); 
     491 
     492    if (options.isGroupFiles()) { 
     493      options.setId(fileStitcher.getFilePattern().getPattern()); 
     494    } 
    453495 
    454496    // NB: This test will fail if the LUT is null before calling openBytes. 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImportStep.java

    r6588 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImportStep.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImportStep.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImportStep.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImportStep.java">SVN</a></dd></dl> 
    3636 */ 
    3737public enum ImportStep { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/Importer.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/Importer.java">SVN</a></dd></dl> 
    4444 * 
    4545 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImporterDialog.java

    r6588 r7047  
    3434 * 
    3535 * <dl><dt><b>Source code:</b></dt> 
    36  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">Trac</a>, 
    37  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">SVN</a></dd></dl> 
     36 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">Trac</a>, 
     37 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/FilePatternDialog.java">SVN</a></dd></dl> 
    3838 */ 
    3939public abstract class ImporterDialog extends OptionsDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImporterMetadata.java

    r6588 r7047  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">Trac</a>, 
    42  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterMetadata.java">SVN</a></dd></dl> 
    4343 */ 
    4444public class ImporterMetadata extends HashMap<String, Object> { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImporterOptions.java

    r6659 r7047  
    4444 * 
    4545 * <dl><dt><b>Source code:</b></dt> 
    46  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">Trac</a>, 
    47  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">SVN</a></dd></dl> 
     46 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">Trac</a>, 
     47 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java">SVN</a></dd></dl> 
    4848 */ 
    4949public class ImporterOptions extends OptionsList { 
     
    6565  public static final String KEY_QUIET           = "quiet"; 
    6666  //public static final String KEY_RECORD          = "record"; 
    67   public static final String KEY_SERIES          = "series"; 
    6867  public static final String KEY_SHOW_METADATA   = "showMetadata"; 
    6968  public static final String KEY_SHOW_OME_XML    = "showOMEXML"; 
     
    196195  /** Handles obsolete macro keys, for backward compatibility. */ 
    197196  public void checkObsoleteOptions() { 
    198     String options = Macro.getOptions(); 
     197    final String macroOptions = Macro.getOptions(); 
    199198 
    200199    // NB: It would be nice to remove the Standard ImageJ option someday; 
    201200    // when that happens, the following code provides support for old macros. 
    202201    // check obsolete view options 
    203     //String stackFormat = options == null ? 
    204     //  null : Macro.getValue(options, "view", null); 
     202    //String stackFormat = macroOptions == null ? 
     203    //  null : Macro.getValue(macroOptions, "view", null); 
    205204    //final String viewStandard = "Standard ImageJ"; 
    206205    //if (viewStandard.equals(stackFormat)) { 
    207206    //  // Standard ImageJ -> Hyperstack 
    208     //  options = options.replaceFirst( 
     207    //  macroOptions = macroOptions.replaceFirst( 
    209208    //    "\\[" + viewStandard + "\\]", VIEW_HYPERSTACK); 
    210     //  Macro.setOptions(options); 
     209    //  Macro.setOptions(macroOptions); 
    211210    //  setStackFormat(VIEW_HYPERSTACK); 
    212211    //} 
    213212 
    214213    // check obsolete color options 
    215     boolean mergeChannels = checkKey(options, "merge_channels"); 
    216     boolean rgbColorize = checkKey(options, "rgb_colorize"); 
    217     boolean customColorize = checkKey(options, "custom_colorize"); 
     214    final boolean mergeChannels = checkKey(macroOptions, "merge_channels"); 
     215    final boolean rgbColorize = checkKey(macroOptions, "rgb_colorize"); 
     216    final boolean customColorize = checkKey(macroOptions, "custom_colorize"); 
    218217    if (mergeChannels) setColorMode(COLOR_MODE_COMPOSITE); 
    219218    else if (rgbColorize) setColorMode(COLOR_MODE_COLORIZED); 
     
    307306  //public void setRecord(boolean b) { setValue(KEY_RECORD, b); } 
    308307 
    309   // series 
    310   public String getSeriesInfo() { return getInfo(KEY_SERIES); } 
    311   public String getSeries() { return getValue(KEY_SERIES); } 
    312   public void setSeries(String s) { setValue(KEY_SERIES, s); } 
    313  
    314308  // showMetadata 
    315309  public String getShowMetadataInfo() { return getInfo(KEY_SHOW_METADATA); } 
     
    404398  public void setSeriesOn(int s, boolean value) { 
    405399    set(seriesOn, s, value, false); 
     400  } 
     401  public void clearSeries() { 
     402    seriesOn.clear(); 
    406403  } 
    407404 
     
    486483 
    487484  /** Tests whether the given boolean key is set in the specified options. */ 
    488   private boolean checkKey(String options, String key) { 
     485  protected boolean checkKey(String options, String key) { 
    489486    if (options == null) return false; 
    490487 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ImporterPrompter.java

    r6654 r7047  
    4444 * 
    4545 * <dl><dt><b>Source code:</b></dt> 
    46  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterPrompter.java">Trac</a>, 
    47  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterPrompter.java">SVN</a></dd></dl> 
     46 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ImporterPrompter.java">Trac</a>, 
     47 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ImporterPrompter.java">SVN</a></dd></dl> 
    4848 */ 
    4949public class ImporterPrompter implements StatusListener { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/LocationDialog.java

    r6588 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/LocationDialog.java">SVN</a></dd></dl> 
    3636 */ 
    3737public class LocationDialog extends ImporterDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/MainDialog.java

    r6704 r7047  
    5757 * 
    5858 * <dl><dt><b>Source code:</b></dt> 
    59  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/MainDialog.java">Trac</a>, 
    60  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/MainDialog.java">SVN</a></dd></dl> 
     59 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/MainDialog.java">Trac</a>, 
     60 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/MainDialog.java">SVN</a></dd></dl> 
    6161 */ 
    6262public class MainDialog extends ImporterDialog 
     
    520520 
    521521    // colorModeChoice 
    522     colorModeEnabled = !isStackImage5D && !isStackView5D; 
     522    colorModeEnabled = !isStackImage5D && !isStackView5D && !isStackStandard; 
    523523    if (!colorModeEnabled) colorModeValue = ImporterOptions.COLOR_MODE_DEFAULT; 
    524524 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/MemoryDialog.java

    r6654 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/MemoryDialog.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/MemoryDialog.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/MemoryDialog.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/MemoryDialog.java">SVN</a></dd></dl> 
    3636 */ 
    3737public class MemoryDialog extends ImporterDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/RangeDialog.java

    r6654 r7047  
    3434 * 
    3535 * <dl><dt><b>Source code:</b></dt> 
    36  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">Trac</a>, 
    37  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">SVN</a></dd></dl> 
     36 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">Trac</a>, 
     37 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/RangeDialog.java">SVN</a></dd></dl> 
    3838 */ 
    3939public class RangeDialog extends ImporterDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/SeriesDialog.java

    r6660 r7047  
    3030import com.jgoodies.forms.layout.FormLayout; 
    3131 
     32import ij.Macro; 
    3233import ij.gui.GenericDialog; 
    3334 
     
    4243import java.awt.event.ActionEvent; 
    4344import java.awt.event.ActionListener; 
    44 import java.util.StringTokenizer; 
    4545 
    4646import javax.swing.Box; 
     
    5454 * 
    5555 * <dl><dt><b>Source code:</b></dt> 
    56  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">Trac</a>, 
    57  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">SVN</a></dd></dl> 
     56 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">Trac</a>, 
     57 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SeriesDialog.java">SVN</a></dd></dl> 
    5858 */ 
    5959public class SeriesDialog extends ImporterDialog implements ActionListener { 
     
    6363  public static final int MAX_COMPONENTS = 256; 
    6464  public static final int MAX_SERIES_THUMBS = 200; 
     65  public static final int MAX_SERIES_TOGGLES = MAX_SERIES_THUMBS; 
    6566 
    6667  // -- Fields -- 
     
    8182  @Override 
    8283  protected boolean needPrompt() { 
    83     // CTR FIXME - eliminate weird handling of series string here 
    84     String seriesString = options.getSeries(); 
    85     if (process.isWindowless()) { 
    86       if (seriesString != null) { 
    87         if (seriesString.startsWith("[")) { 
    88           seriesString = seriesString.substring(1, seriesString.length() - 2); 
    89         } 
    90  
    91         // default all series to false 
    92         final int seriesCount = process.getSeriesCount(); 
    93         for (int s=0; s<seriesCount; s++) options.setSeriesOn(s, false); 
    94  
    95         // extract enabled series values from series string 
    96         StringTokenizer tokens = new StringTokenizer(seriesString, " "); 
    97         while (tokens.hasMoreTokens()) { 
    98           String token = tokens.nextToken().trim(); 
    99           int n = Integer.parseInt(token); 
    100           if (n < seriesCount) options.setSeriesOn(n, true); 
    101         } 
    102       } 
    103       options.setSeries(seriesString); 
    104       return false; 
    105     } 
    106  
    107     return process.getSeriesCount() > 1 && 
     84    return !process.isWindowless() && process.getSeriesCount() > 1 && 
    10885      !options.openAllSeries() && !options.isViewNone(); 
    10986  } 
     
    11188  @Override 
    11289  protected GenericDialog constructDialog() { 
    113     // -- CTR FIXME - refactor series-related options into SeriesOptions class 
    114     // has a normalize(IFormatReader) method 
    115     // call both before and after the dialog here... 
    116  
    11790    final int seriesCount = process.getSeriesCount(); 
    11891 
     
    139112    GenericDialog gd = new GenericDialog("Bio-Formats Series Options"); 
    140113 
    141     // NB: We need to add the checkboxes in groups, to prevent an 
    142     // exception from being thrown if there are more than 512 series. 
    143     // See also: 
    144     //   https://skyking.microscopy.wisc.edu/trac/java/ticket/408 and 
    145     //   http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980 
    146  
    147     final int nGroups = (seriesCount + MAX_COMPONENTS - 1) / MAX_COMPONENTS; 
    148     int nextSeries = 0; 
    149     for (int i=0; i<nGroups; i++) { 
    150       final int nRows = Math.min(MAX_COMPONENTS, seriesCount - nextSeries); 
    151       final String[] labels = new String[nRows]; 
    152       final boolean[] defaultValues = new boolean[nRows]; 
    153       for (int row=0; row<nRows; row++) { 
    154         labels[row] = process.getSeriesLabel(nextSeries); 
    155         defaultValues[row] = options.isSeriesOn(nextSeries); 
    156         nextSeries++; 
    157       } 
    158       gd.addCheckboxGroup(nRows, 1, labels, defaultValues); 
    159     } 
    160  
    161     // extract checkboxes, for "Select All" and "Deselect All" functions 
    162     boxes = WindowTools.getCheckboxes(gd).toArray(new Checkbox[0]); 
    163  
    164     // rebuild dialog so that the thumbnails and checkboxes line up correctly 
    165     rebuildDialog(gd, nGroups); 
     114    // NB: Provide individual checkboxes only when series count is manageable. 
     115    if (seriesCount < MAX_SERIES_TOGGLES) { 
     116      // NB: We need to add the checkboxes in groups, to prevent an 
     117      // exception from being thrown if there are more than 512 series. 
     118      // See also: 
     119      //   http://dev.loci.wisc.edu/trac/java/ticket/408 and 
     120      //   http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980 
     121 
     122      final int nGroups = (seriesCount + MAX_COMPONENTS - 1) / MAX_COMPONENTS; 
     123      int nextSeries = 0; 
     124      for (int i=0; i<nGroups; i++) { 
     125        final int nRows = Math.min(MAX_COMPONENTS, seriesCount - nextSeries); 
     126        final String[] labels = new String[nRows]; 
     127        final boolean[] defaultValues = new boolean[nRows]; 
     128        for (int row=0; row<nRows; row++) { 
     129          labels[row] = process.getSeriesLabel(nextSeries); 
     130          defaultValues[row] = options.isSeriesOn(nextSeries); 
     131          nextSeries++; 
     132        } 
     133        gd.addCheckboxGroup(nRows, 1, labels, defaultValues); 
     134      } 
     135 
     136      // extract checkboxes, for "Select All" and "Deselect All" functions 
     137      boxes = WindowTools.getCheckboxes(gd).toArray(new Checkbox[0]); 
     138 
     139      // rebuild dialog so that the thumbnails and checkboxes line up correctly 
     140      rebuildDialog(gd, nGroups); 
     141    } 
     142    else { 
     143      // too many series; display a simple text field for specifying series 
     144      gd.addMessage( 
     145        "Please specify the image series you wish to import.\n" + 
     146        "Use commas to list multiple series. You can also use\n" + 
     147        "a dash to represent a range of series. For example,\n" + 
     148        "to import series 1, 3, 4, 5, 7, 8, 9, 12, 15 & 16,\n" + 
     149        "you could write: 1, 3-5, 7-9, 12, 15-16"); 
     150      gd.addStringField("Series_list: ", "1"); 
     151    } 
    166152 
    167153    return gd; 
     
    183169  protected boolean harvestResults(GenericDialog gd) { 
    184170    final int seriesCount = process.getSeriesCount(); 
    185     String seriesString = "["; 
    186     for (int i=0; i<seriesCount; i++) { 
    187       boolean on = gd.getNextBoolean(); 
    188       options.setSeriesOn(i, on); 
    189       if (on) seriesString += i + " "; 
    190     } 
    191     seriesString += "]"; 
    192     options.setSeries(seriesString); 
     171    options.clearSeries(); 
     172 
     173    // examine series key regardless of number of series 
     174    final String macroOptions = Macro.getOptions(); 
     175    final String macroSeriesList = macroOptions == null ? null : 
     176      Macro.getValue(macroOptions, "series_list", null); 
     177    if (macroSeriesList != null) process.setSeriesList(macroSeriesList); 
     178 
     179    if (seriesCount < MAX_SERIES_TOGGLES) { 
     180      // harvest individual checkbox values 
     181      for (int i=0; i<seriesCount; i++) { 
     182        final boolean on = gd.getNextBoolean(); 
     183        if (on) options.setSeriesOn(i, on); 
     184      } 
     185    } 
     186    else { 
     187      // harvest series string 
     188      final String seriesList = gd.getNextString(); 
     189      process.setSeriesList(seriesList); 
     190    } 
     191 
     192    // examine series_XX keys regardless of number of series 
     193    if (macroOptions != null) { 
     194      for (int i=0; i<seriesCount; i++) { 
     195        final String seriesKey = "series_" + (i + 1); 
     196        final boolean on = options.checkKey(macroOptions, seriesKey); 
     197        if (on) options.setSeriesOn(i, on); 
     198      } 
     199    } 
     200 
    193201    return true; 
    194202  } 
     
    197205 
    198206  public void actionPerformed(ActionEvent e) { 
    199     String cmd = e.getActionCommand(); 
     207    final String cmd = e.getActionCommand(); 
    200208    if ("select".equals(cmd)) { 
    201209      for (int i=0; i<boxes.length; i++) boxes[i].setState(true); 
     
    219227 
    220228  private void rebuildDialog(GenericDialog gd, int buttonRow) { 
    221     // rebuild dialog using FormLayout to organize things more nicely 
     229    // rebuild dialog to organize things more nicely 
    222230 
    223231    final String cols = p == null ? "pref" : "pref, 3dlu, pref"; 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/SwapDialog.java

    r6588 r7047  
    4040 * 
    4141 * <dl><dt><b>Source code:</b></dt> 
    42  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">Trac</a>, 
    43  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">SVN</a></dd></dl> 
     42 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">Trac</a>, 
     43 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/SwapDialog.java">SVN</a></dd></dl> 
    4444 */ 
    4545public class SwapDialog extends ImporterDialog implements ItemListener { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/ThumbLoader.java

    r6660 r7047  
    4747 * 
    4848 * <dl><dt><b>Source code:</b></dt> 
    49  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">Trac</a>, 
    50  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">SVN</a></dd></dl> 
     49 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">Trac</a>, 
     50 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/ThumbLoader.java">SVN</a></dd></dl> 
    5151 */ 
    5252public class ThumbLoader implements Runnable { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/in/UpgradeDialog.java

    r6654 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/in/UpgradeDialog.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class UpgradeDialog extends ImporterDialog { 
     
    7979 
    8080    if (options.doUpgradeCheck()) { 
    81       BF.status(false, "Checking for new version..."); 
     81      BF.status(false, "Checking for new stable version..."); 
    8282      if (Updater.newVersionAvailable()) { 
    8383        boolean doUpgrade = IJ.showMessageWithCancel("", 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/macro/LociFunctions.java

    r6654 r7047  
    5656 * 
    5757 * <dl><dt><b>Source code:</b></dt> 
    58  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/macro/LociFunctions.java">Trac</a>, 
    59  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/macro/LociFunctions.java">SVN</a></dd></dl> 
     58 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/macro/LociFunctions.java">Trac</a>, 
     59 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/macro/LociFunctions.java">SVN</a></dd></dl> 
    6060 * 
    6161 * @author Curtis Rueden ctrueden at wisc.edu 
     
    282282  public void getMetadataValue(String field, String[] value) { 
    283283    Object o = r.getMetadataValue(field); 
     284    value[0] = o == null ? null : o.toString(); 
     285  } 
     286 
     287  public void getSeriesMetadataValue(String field, String[] value) { 
     288    Object o = r.getSeriesMetadataValue(field); 
    284289    value[0] = o == null ? null : o.toString(); 
    285290  } 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/macro/MacroFunctions.java

    r6588 r7047  
    4545 * 
    4646 * <dl><dt><b>Source code:</b></dt> 
    47  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/macro/MacroFunctions.java">Trac</a>, 
    48  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/macro/MacroFunctions.java">SVN</a></dd></dl> 
     47 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/macro/MacroFunctions.java">Trac</a>, 
     48 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/macro/MacroFunctions.java">SVN</a></dd></dl> 
    4949 * 
    5050 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/out/Exporter.java

    r6710 r7047  
    8181 * 
    8282 * <dl><dt><b>Source code:</b></dt> 
    83  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">Trac</a>, 
    84  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">SVN</a></dd></dl> 
     83 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">Trac</a>, 
     84 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/out/Exporter.java">SVN</a></dd></dl> 
    8585 * 
    8686 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/prefs/BooleanOption.java

    r6588 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/BooleanOption.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/BooleanOption.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/BooleanOption.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/BooleanOption.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class BooleanOption extends Option { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/prefs/Option.java

    r6588 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/Option.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/Option.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/Option.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/Option.java">SVN</a></dd></dl> 
    3636 */ 
    3737public abstract class Option { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/prefs/OptionsDialog.java

    r6588 r7047  
    3232 * 
    3333 * <dl><dt><b>Source code:</b></dt> 
    34  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsDialog.java">Trac</a>, 
    35  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsDialog.java">SVN</a></dd></dl> 
     34 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsDialog.java">Trac</a>, 
     35 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsDialog.java">SVN</a></dd></dl> 
    3636 */ 
    3737public abstract class OptionsDialog { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/prefs/OptionsList.java

    r6588 r7047  
    3838 * 
    3939 * <dl><dt><b>Source code:</b></dt> 
    40  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsList.java">Trac</a>, 
    41  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsList.java">SVN</a></dd></dl> 
     40 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsList.java">Trac</a>, 
     41 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/OptionsList.java">SVN</a></dd></dl> 
    4242 */ 
    4343public class OptionsList { 
     
    190190  } 
    191191 
     192  // -- Object API methods -- 
     193 
     194  /* @see java.lang.Object#equals(Object) */ 
     195  public boolean equals(Object o) { 
     196    if (o == null || !(o instanceof OptionsList)) return false; 
     197    OptionsList optionsList = (OptionsList) o; 
     198    if (options.size() != optionsList.options.size()) { 
     199      return false; 
     200    } 
     201    for (String key : options.keySet()) { 
     202      Option a = options.get(key); 
     203      Option b = optionsList.options.get(key); 
     204      if ((a != null && b == null) || (a == null && b != null)) { 
     205        return false; 
     206      } 
     207      else if (a == null && b == null) continue; 
     208 
     209      if ((a instanceof BooleanOption) && (b instanceof BooleanOption)) { 
     210        if (((BooleanOption) a).getValue() != ((BooleanOption) b).getValue()) { 
     211          return false; 
     212        } 
     213      } 
     214      else if ((a instanceof StringOption) && (b instanceof StringOption)) { 
     215        String aValue = ((StringOption) a).getValue(); 
     216        String bValue = ((StringOption) b).getValue(); 
     217        if (aValue == null && bValue == null) continue; 
     218        if (aValue == null) { 
     219          return false; 
     220        } 
     221        if (aValue == null || !aValue.equals(bValue)) { 
     222          return false; 
     223        } 
     224      } 
     225      else { 
     226        return false; 
     227      } 
     228    } 
     229    return true; 
     230  } 
     231 
    192232} 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/prefs/StringOption.java

    r6588 r7047  
    3737 * 
    3838 * <dl><dt><b>Source code:</b></dt> 
    39  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/StringOption.java">Trac</a>, 
    40  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/StringOption.java">SVN</a></dd></dl> 
     39 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/prefs/StringOption.java">Trac</a>, 
     40 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/prefs/StringOption.java">SVN</a></dd></dl> 
    4141 */ 
    4242public class StringOption extends Option { 
     
    139139  /* @see Option#parseOption(String arg) */ 
    140140  public void parseOption(String arg) { 
    141     value = Macro.getValue(arg, key, value); 
    142     if (value == null && label != null) { 
     141    String keyValue = Macro.getValue(arg, key, value); 
     142    if ((value == null || keyValue.equals(value)) && label != null) { 
    143143      value = Macro.getValue(arg, label, value); 
    144144    } 
     145    else value = keyValue; 
    145146  } 
    146147 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/shortcut/ShortcutPanel.java

    r6698 r7047  
    5656 * 
    5757 * <dl><dt><b>Source code:</b></dt> 
    58  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ShortcutPanel.java">Trac</a>, 
    59  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ShortcutPanel.java">SVN</a></dd></dl> 
     58 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ShortcutPanel.java">Trac</a>, 
     59 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ShortcutPanel.java">SVN</a></dd></dl> 
    6060 * 
    6161 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/shortcut/ShortcutTransferHandler.java

    r6588 r7047  
    4242 * 
    4343 * <dl><dt><b>Source code:</b></dt> 
    44  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ShortcutTransferHandler.java">Trac</a>, 
    45  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ShortcutTransferHandler.java">SVN</a></dd></dl> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ShortcutTransferHandler.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ShortcutTransferHandler.java">SVN</a></dd></dl> 
    4646 * 
    4747 * @author Curtis Rueden ctrueden at wisc.edu 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/BFVirtualStack.java

    r6658 r7047  
    4848 * 
    4949 * <dl><dt><b>Source code:</b></dt> 
    50  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/BFVirtualStack.java">Trac</a>, 
    51  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/BFVirtualStack.java">SVN</a></dd></dl> 
     50 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/BFVirtualStack.java">Trac</a>, 
     51 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/BFVirtualStack.java">SVN</a></dd></dl> 
    5252 * 
    5353 * @author Melissa Linkert melissa at glencoesoftware.com 
     
    7575  // -- Static utility methods -- 
    7676 
    77   protected static int getWidth(IFormatReader r, String path) 
     77  protected static int getWidth(IFormatReader r, String path, int series) 
    7878    throws FormatException, IOException 
    7979  { 
    80     r.setId(path); 
     80    r.setSeries(series); 
    8181    return r.getSizeX(); 
    8282  } 
    8383 
    84   protected static int getHeight(IFormatReader r, String path) 
     84  protected static int getHeight(IFormatReader r, String path, int series) 
    8585    throws FormatException, IOException 
    8686  { 
    87     r.setId(path); 
     87    r.setSeries(series); 
    8888    return r.getSizeY(); 
    8989  } 
     
    9595    throws FormatException, IOException, CacheException 
    9696  { 
    97     super(getWidth(r, path), getHeight(r, path), null, path); 
     97    super(getWidth(r, path, r.getSeries()), getHeight(r, path, r.getSeries()), 
     98      null, path); 
    9899    reader = new ImageProcessorReader(r); 
    99100    id = path; 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/BrowserOptionsWindow.java

    r6588 r7047  
    3838 * 
    3939 * <dl><dt><b>Source code:</b></dt> 
    40  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/BrowserOptionsWindow.java">Trac</a>, 
    41  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/BrowserOptionsWindow.java">SVN</a></dd></dl> 
     40 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/BrowserOptionsWindow.java">Trac</a>, 
     41 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/BrowserOptionsWindow.java">SVN</a></dd></dl> 
    4242 */ 
    4343public class BrowserOptionsWindow extends JFrame { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/DataBrowser.java

    r6654 r7047  
    6767 * 
    6868 * <dl><dt><b>Source code:</b></dt> 
    69  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/DataBrowser.java">Trac</a>, 
    70  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/DataBrowser.java">SVN</a></dd></dl> 
     69 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/DataBrowser.java">Trac</a>, 
     70 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/DataBrowser.java">SVN</a></dd></dl> 
    7171 */ 
    7272public class DataBrowser extends StackWindow { 
     
    342342              int sizeT = tSlider.getMaximum() - 1; 
    343343              if (t > sizeT) t = 1; 
    344               setPosition(c, z, t); 
    345344              imp.setPosition(c, z, t); 
    346345              syncSliders(); 
    347 //              updateSlice(); 
    348346              int fps = ((Number) fpsSpin.getValue()).intValue(); 
    349347              ms = 1000 / fps; 
     
    500498    int t = tScroll == null ? 1 : tScroll.getValue(); 
    501499    setPosition(c, z, t); 
    502 //    updateSlice(); 
     500    imp.setPosition(c, z, t); 
    503501  } 
    504502 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/IJStatusEchoer.java

    r6588 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/IJStatusEchoer.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/IJStatusEchoer.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/IJStatusEchoer.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/IJStatusEchoer.java">SVN</a></dd></dl> 
    3939 */ 
    4040public class IJStatusEchoer extends AppenderSkeleton { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/ImageProcessorReader.java

    r6714 r7047  
    4747 * 
    4848 * <dl><dt><b>Source code:</b></dt> 
    49  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorReader.java">Trac</a>, 
    50  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorReader.java">SVN</a></dd></dl> 
     49 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorReader.java">Trac</a>, 
     50 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorReader.java">SVN</a></dd></dl> 
    5151 */ 
    5252public class ImageProcessorReader extends ReaderWrapper { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/ImageProcessorSource.java

    r6588 r7047  
    3939 * 
    4040 * <dl><dt><b>Source code:</b></dt> 
    41  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorSource.java">Trac</a>, 
    42  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorSource.java">SVN</a></dd></dl> 
     41 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorSource.java">Trac</a>, 
     42 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ImageProcessorSource.java">SVN</a></dd></dl> 
    4343 */ 
    4444public class ImageProcessorSource implements ICacheSource { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/LibraryChecker.java

    r6773 r7047  
    3636 * 
    3737 * <dl><dt><b>Source code:</b></dt> 
    38  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LibraryChecker.java">Trac</a>, 
    39  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LibraryChecker.java">SVN</a></dd></dl> 
     38 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LibraryChecker.java">Trac</a>, 
     39 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LibraryChecker.java">SVN</a></dd></dl> 
    4040 */ 
    4141public final class LibraryChecker { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/LociPrefs.java

    r6588 r7047  
    4141 * 
    4242 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LociPrefs.java">Trac</a>, 
    44  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LociPrefs.java">SVN</a></dd></dl> 
     43 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LociPrefs.java">Trac</a>, 
     44 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LociPrefs.java">SVN</a></dd></dl> 
    4545 */ 
    4646public final class LociPrefs { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/LuraWave.java

    r6716 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LuraWave.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LuraWave.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/LuraWave.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/LuraWave.java">SVN</a></dd></dl> 
    3939 */ 
    4040public final class LuraWave { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/ROIHandler.java

    r6702 r7047  
    5757 * 
    5858 * <dl><dt><b>Source code:</b></dt> 
    59  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ROIHandler.java">Trac</a>, 
    60  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ROIHandler.java">SVN</a></dd></dl> 
     59 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/ROIHandler.java">Trac</a>, 
     60 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/ROIHandler.java">SVN</a></dd></dl> 
    6161 * 
    6262 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/RecordedImageProcessor.java

    r6654 r7047  
    5656 * 
    5757 * <dl><dt><b>Source code:</b></dt> 
    58  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java">Trac</a>, 
    59  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java">SVN</a></dd></dl> 
     58 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java">Trac</a>, 
     59 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/RecordedImageProcessor.java">SVN</a></dd></dl> 
    6060 * 
    6161 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/SearchableWindow.java

    r6588 r7047  
    5353 * 
    5454 * <dl><dt><b>Source code:</b></dt> 
    55  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/SearchableWindow.java">Trac</a>, 
    56  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/SearchableWindow.java">SVN</a></dd></dl> 
     55 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/SearchableWindow.java">Trac</a>, 
     56 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/SearchableWindow.java">SVN</a></dd></dl> 
    5757 */ 
    5858public class SearchableWindow extends TextWindow { 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/VirtualImagePlus.java

    r6588 r7047  
    2929import ij.ImageStack; 
    3030import ij.process.ImageStatistics; 
     31import ij.process.LUT; 
    3132 
    3233import java.io.IOException; 
     
    4142 * 
    4243 * <dl><dt><b>Source code:</b></dt> 
    43  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/VirtualImagePlus.java">Trac</a>, 
    44  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/VirtualImagePlus.java">SVN</a></dd></dl> 
     44 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/VirtualImagePlus.java">Trac</a>, 
     45 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/VirtualImagePlus.java">SVN</a></dd></dl> 
    4546 * 
    4647 * @author Melissa Linkert melissa at glencoesoftware.com 
     
    5152 
    5253  private IFormatReader r; 
     54  private LUT[] luts; 
    5355 
    5456  // -- Constructor -- 
     
    6567  public void setReader(IFormatReader r) { 
    6668    this.r = r; 
     69  } 
     70 
     71  public void setLUTs(LUT[] luts) { 
     72    this.luts = luts; 
    6773  } 
    6874 
     
    8389      // to GRAY32 (regardless of the actual processor type) 
    8490      setProcessor(getTitle(), proc.getChild()); 
     91      int channel = getChannel() - 1; 
     92      if (channel >= 0 && luts != null && channel < luts.length) { 
     93        getProcessor().setColorModel(luts[channel]); 
     94      } 
    8595      this.ip = proc; 
    8696    } 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/VirtualReader.java

    r6588 r7047  
    3535 * 
    3636 * <dl><dt><b>Source code:</b></dt> 
    37  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/VirtualReader.java">Trac</a>, 
    38  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/VirtualReader.java">SVN</a></dd></dl> 
     37 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/VirtualReader.java">Trac</a>, 
     38 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/VirtualReader.java">SVN</a></dd></dl> 
    3939 * 
    4040 * @author Melissa Linkert melissa at glencoesoftware.com 
  • branches/maven/projects/loci-plugins/src/main/java/loci/plugins/util/WindowTools.java

    r6588 r7047  
    5656 * 
    5757 * <dl><dt><b>Source code:</b></dt> 
    58  * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java">Trac</a>, 
    59  * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java">SVN</a></dd></dl> 
     58 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java">Trac</a>, 
     59 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/util/WindowTools.java">SVN</a></dd></dl> 
    6060 */ 
    6161public final class WindowTools { 
  • branches/maven/projects/loci-plugins/src/main/resources/loci/plugins/config/libraries.txt

  • branches/maven/projects/loci-plugins/src/main/resources/loci/plugins/in/importer-options.txt

    r6776 r7047  
    168168#  <br><br>When viewing as a virtual stack with this option enabled,      \ 
    169169#  Bio-Formats will attempt to record the operations you perform. When    \ 
    170 #  you switch to a new image plane, Bio-Formats will \"play back\" those  \ 
     170#  you switch to a new image plane, Bio-Formats will "play back" those    \ 
    171171#  same operations, so that the image plane undergoes the same processing \ 
    172172#  you performed previously. In this way, the image stack should behave   \ 
     
    174174#default = false 
    175175 
    176 [series] 
    177 type = string 
    178 label = series 
    179 default = 0 
    180  
    181176[showMetadata] 
    182177type = boolean 
    183 label = Display_metadata in results window 
    184 info = <b>Display metadata in results window</b> - \ 
     178label = Display_metadata 
     179info = <b>Display metadata</b> - \ 
    185180  Reads metadata that may be contained within the file format and      \ 
    186181  displays it. You can save it as a text file or copy it from the File \ 
    187   and Edit menus specific to the ImageJ Results window. Readability    \ 
    188   depends upon the manner in which metadata is formatted in the data   \ 
    189   source. 
     182  and Edit menus specific to the "Original Metadata" window.           \ 
     183  Readability depends upon the manner in which metadata is formatted   \ 
     184  in the data source. The metadata can also be displayed by pressing   \ 
     185  "i" (Image &gt; Show Info) when the imported image is active. 
    190186default = false 
    191187 
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